Abstract 1259: PD-L1 expression by RNA-sequencing and survival from pembrolizumab in non-small cell lung cancer (NSCLC)
Authors: Mary K. Nesline, Sarabjot Pabla, Yong Hee Lee, Paul DePietro, Amy Early, Roger Klein, Shengle Zhang, Jeffrey Conroy
Journal: Cancer Research (2022)

Abstract PURPOSE: The immunohistochemistry companion diagnostic test for pembrolizumab (IHC 22C3 pharmDx) lacks sensitivity, challenging immunotherapy selection for NSCLC patients with lower levels of expression. Unlike IHC 22C3, which restricts assessment of PD-L1 expression to viable tumor cells as a tumor proportion score (% TPS), mRNA next generation sequencing (RNA-seq) measures PD-L1 expression in the tumor microenvironment for both tumor and inflammatory background cells. RNA-seq previously demonstrated concordance with IHC and may be a robust alternative testing method for multiple tumor types. Here, we sought to optimize PD-L1 RNA-seq cutoff values in NSCLC to improve clinical sensitivity. PROCEDURE: NSCLC patients included in the study (n=3,465) were tested for PD-L1 expression by IHC 22C3 and clinically validated RNA-seq, measured as % rank (0-100) relative to a reference population based on normalized reads per million (nRPM). Patients were divided into an RNA-seq cut-off discovery cohort (n=3,168), and a test cohort pembrolizumab treated patients. Principal components analysis (PCA) was used to classify patients based on test results and explore cut-off values in the discovery cohort. Kaplan Meier curves and a Cox proportional hazards regression models assessed overall survival (OS) hazard ratios (HR) for RNA-seq versus standard of care IHC cut-offs in the test cohort. RESULTS: Unsupervised PCA clustering identified three distinct PD-L1 groups separated by combinations of significant over- and under-representation of RNA-seq and IHC result measures from prior testing. The groups were labeled as “low” (rank ≤40), “moderate” (rank 41-73), and “high” (rank ≥74), based on the median RNA-seq rank for each group (+/- 1SD for low and high). Both the low and moderate groups were overrepresented by patients in the PD-L1 IHC low and negative groups. The moderate group was overrepresented by patients with moderately high PD-L1 RNA-seq ranks (median=70), while the low group was overrepresented by patients that were not PD-L1 high by RNA-seq. The high group was overrepresented by patients high for PD-L1 by both IHC and RNA-seq. OS HRs were better for RNA-seq high versus moderate (HR=0.05, CI 0.00-0.63, p=.02), and RNA-seq high versus low (HR=0.16, CI 0.03-0.86, p=.03) groups compared to standard of care IHC 22C3 high versus low groups, (HR=0.21, CI 0.04-1.07, p=.06). Findings were non-significant for the RNA-seq moderate versus low groups, likely due to the limited and disproportionately high number of patients with poor performance status in these groups. CONCLUSIONS: PD-L1 expression by RNA-seq demonstrated improved clinical sensitivity in predicting OS versus standard of care PD-LI IHC in a pembrolizumab treated NSCLC patient cohort. Additional studies are needed to further define cut-offs in the context of performance status, and better understand immune escape mechanisms in the moderate group. Citation Format: Mary K. Nesline, Sarabjot Pabla, Yong Hee Lee, Paul DePietro, Amy Early, Roger Klein, Shengle Zhang, Jeffrey Conroy. PD-L1 expression by RNA-sequencing and survival from pembrolizumab in non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1259.